Yes your right about black hat techniques.
It depends some sites dont need to do link exchanges cos people want to link to there sites anyways. Sites with helpful info such as tutorials and how to pages automatically get loads of links.
Then your can also get links though directory submissions which means you dont need to have links back to there sites, same with article submission or if you buy links.
Large sites tend to have a smaller site(s) and do three way link exchanges, so A links to B and B links to C that way C never links to anybody.
Then yes some sites will even have a directory for link exchnages but hide it. (bit naughty though really). Directory or links pages (Resource page or anything else they have called it) should be linked to by the home page really.